1
|
Zhou B, Wan F, Lei KX, Lan P, Wu J, Lei M. Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes. J Biol Chem 2024; 300:105729. [PMID: 38336296 PMCID: PMC10966300 DOI: 10.1016/j.jbc.2024.105729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.
Collapse
Affiliation(s)
- Bin Zhou
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Futang Wan
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Kevin X Lei
- Shanghai High School International Division, Shanghai, China
| | - Pengfei Lan
- Shanghai Institute of Precision Medicine, Shanghai, China; Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
2
|
Guegler CK, Teodoro GIC, Srikant S, Chetlapalli K, Doering CR, Ghose DA, Laub MT. A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin-antitoxin system. Nucleic Acids Res 2024; 52:1298-1312. [PMID: 38117986 PMCID: PMC10853763 DOI: 10.1093/nar/gkad1207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which are poorly understood. In T4-like phages, the gene tifA prevents bacterial defense by the type III toxin-antitoxin (TA) system toxIN, but the mechanism by which TifA inhibits ToxIN remains unclear. Here, we show that TifA directly binds both the endoribonuclease ToxN and RNA, leading to the formation of a high molecular weight ribonucleoprotein complex in which ToxN is inhibited. The RNA binding activity of TifA is necessary for its interaction with and inhibition of ToxN. Thus, we propose that TifA inhibits ToxN during phage infection by trapping ToxN on cellular RNA, particularly the abundant 16S rRNA, thereby preventing cleavage of phage transcripts. Taken together, our results reveal a novel mechanism underlying inhibition of a phage-defensive RNase toxin by a small, phage-encoded protein.
Collapse
Affiliation(s)
- Chantal K Guegler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriella I C Teodoro
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keerthana Chetlapalli
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher R Doering
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dia A Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
García-Montoya C, García-Linares S, Heras-Márquez D, Majnik M, Laxalde-Fernández D, Amigot-Sánchez R, Martínez-Del-Pozo Á, Palacios-Ortega J. The interaction of the ribotoxin α-sarcin with complex model lipid vesicles. Arch Biochem Biophys 2024; 751:109836. [PMID: 38000493 DOI: 10.1016/j.abb.2023.109836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Fungal ribotoxins are extracellular RNases that inactivate ribosomes by cleaving a single phosphodiester bond at the universally conserved sarcin-ricin loop of the large rRNA. However, to reach the ribosomes, they need to cross the plasma membrane. It is there where these toxins show their cellular specificity, being especially active against tumoral or virus-infected cells. Previous studies have shown that fungal ribotoxins interact with negatively charged membranes, typically containing phosphatidylserine or phosphatidylglycerol. This ability is rooted on their long, non-structured, positively charged loops, and its N-terminal β-hairpin. However, its effect on complex lipid mixtures, including sphingophospholipids or cholesterol, remains poorly studied. Here, wild-type α-sarcin was used to evaluate its interaction with a variety of membranes not assayed before, which resemble much more closely mammalian cell membranes. The results confirm that α-sarcin is particularly sensitive to charge density on the vesicle surface. Its ability to induce vesicle aggregation is strongly influenced by both the lipid headgroup and the degree of saturation of the fatty acid chains. Acyl chain length is indeed particularly important for lipid mixing. Finally, cholesterol plays an important role in diluting the concentration of available negative charges and modulates the ability of α-sarcin to cross the membrane.
Collapse
Affiliation(s)
- Carmen García-Montoya
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Sara García-Linares
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Diego Heras-Márquez
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Manca Majnik
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | | | - Rafael Amigot-Sánchez
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | | | - Juan Palacios-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| |
Collapse
|
4
|
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas Č, Siksnys V, Tamulaitis G. Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science 2023; 382:1036-1041. [PMID: 38033086 DOI: 10.1126/science.adj2107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023]
Abstract
Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cAn) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cAn-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA4), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA4 complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.
Collapse
Affiliation(s)
- Irmantas Mogila
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Konstanty Keda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| |
Collapse
|
5
|
Podvalnaya N, Bronkhorst AW, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S, Ketting RF. piRNA processing by a trimeric Schlafen-domain nuclease. Nature 2023; 622:402-409. [PMID: 37758951 PMCID: PMC10567574 DOI: 10.1038/s41586-023-06588-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Transposable elements are genomic parasites that expand within and spread between genomes1. PIWI proteins control transposon activity, notably in the germline2,3. These proteins recognize their targets through small RNA co-factors named PIWI-interacting RNAs (piRNAs), making piRNA biogenesis a key specificity-determining step in this crucial genome immunity system. Although the processing of piRNA precursors is an essential step in this process, many of the molecular details remain unclear. Here, we identify an endoribonuclease, precursor of 21U RNA 5'-end cleavage holoenzyme (PUCH), that initiates piRNA processing in the nematode Caenorhabditis elegans. Genetic and biochemical studies show that PUCH, a trimer of Schlafen-like-domain proteins (SLFL proteins), executes 5'-end piRNA precursor cleavage. PUCH-mediated processing strictly requires a 7-methyl-G cap (m7G-cap) and a uracil at position three. We also demonstrate how PUCH interacts with PETISCO, a complex that binds to piRNA precursors4, and that this interaction enhances piRNA production in vivo. The identification of PUCH concludes the search for the 5'-end piRNA biogenesis factor in C. elegans and uncovers a type of RNA endonuclease formed by three SLFL proteins. Mammalian Schlafen (SLFN) genes have been associated with immunity5, exposing a molecular link between immune responses in mammals and deeply conserved RNA-based mechanisms that control transposable elements.
Collapse
Affiliation(s)
- Nadezda Podvalnaya
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | - Alfred W Bronkhorst
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
| | - Raffael Lichtenberger
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Svenja Hellmann
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
| | - Emily Nischwitz
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
- Quantitative Proteomics group, Institute of Molecular Biology, Mainz, Germany
| | - Torben Falk
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- Institute of Molecular Virology and Cell Biology, Friedrich Loeffler Institute, Greifswald, Germany
| | - Sebastian Falk
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria.
| | - René F Ketting
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany.
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Mainz, Germany.
| |
Collapse
|
6
|
Noro I, Bettin I, Fasoli S, Smania M, Lunardi L, Giannini M, Andreoni L, Montioli R, Gotte G. Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus. Int J Biol Macromol 2023; 249:126110. [PMID: 37536419 DOI: 10.1016/j.ijbiomac.2023.126110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.
Collapse
Affiliation(s)
- Irene Noro
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Luca Lunardi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Michele Giannini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Leonardo Andreoni
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| |
Collapse
|
7
|
Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. New insights into RNA processing by the eukaryotic tRNA splicing endonuclease. J Biol Chem 2023; 299:105138. [PMID: 37544645 PMCID: PMC10485636 DOI: 10.1016/j.jbc.2023.105138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
Through its role in intron cleavage, tRNA splicing endonuclease (TSEN) plays a critical function in the maturation of intron-containing pre-tRNAs. The catalytic mechanism and core requirement for this process is conserved between archaea and eukaryotes, but for decades, it has been known that eukaryotic TSENs have evolved additional modes of RNA recognition, which have remained poorly understood. Recent research identified new roles for eukaryotic TSEN, including processing or degradation of additional RNA substrates, and determined the first structures of pre-tRNA-bound human TSEN complexes. These recent discoveries have changed our understanding of how the eukaryotic TSEN targets and recognizes substrates. Here, we review these recent discoveries, their implications, and the new questions raised by these findings.
Collapse
Affiliation(s)
- Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
| | - Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National, Institutes of Health, Research Triangle Park, North Carolina, USA.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA.
| |
Collapse
|
8
|
Tong Y, Lee Y, Liu X, Childs-Disney JL, Suresh BM, Benhamou RI, Yang C, Li W, Costales MG, Haniff HS, Sievers S, Abegg D, Wegner T, Paulisch TO, Lekah E, Grefe M, Crynen G, Van Meter M, Wang T, Gibaut QMR, Cleveland JL, Adibekian A, Glorius F, Waldmann H, Disney MD. Programming inactive RNA-binding small molecules into bioactive degraders. Nature 2023; 618:169-179. [PMID: 37225982 PMCID: PMC10232370 DOI: 10.1038/s41586-023-06091-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Target occupancy is often insufficient to elicit biological activity, particularly for RNA, compounded by the longstanding challenges surrounding the molecular recognition of RNA structures by small molecules. Here we studied molecular recognition patterns between a natural-product-inspired small-molecule collection and three-dimensionally folded RNA structures. Mapping these interaction landscapes across the human transcriptome defined structure-activity relationships. Although RNA-binding compounds that bind to functional sites were expected to elicit a biological response, most identified interactions were predicted to be biologically inert as they bind elsewhere. We reasoned that, for such cases, an alternative strategy to modulate RNA biology is to cleave the target through a ribonuclease-targeting chimera, where an RNA-binding molecule is appended to a heterocycle that binds to and locally activates RNase L1. Overlay of the substrate specificity for RNase L with the binding landscape of small molecules revealed many favourable candidate binders that might be bioactive when converted into degraders. We provide a proof of concept, designing selective degraders for the precursor to the disease-associated microRNA-155 (pre-miR-155), JUN mRNA and MYC mRNA. Thus, small-molecule RNA-targeted degradation can be leveraged to convert strong, yet inactive, binding interactions into potent and specific modulators of RNA function.
Collapse
Affiliation(s)
- Yuquan Tong
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Yeongju Lee
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Xiaohui Liu
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Blessy M Suresh
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Chunying Yang
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Weimin Li
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Matthew G Costales
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Tristan Wegner
- Organisch-Chemisches Institut, University of Münster, Münster, Germany
| | | | - Elizabeth Lekah
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Maison Grefe
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Montina Van Meter
- Histology Core, The Scripps Research Institute and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Tenghui Wang
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Quentin M R Gibaut
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Frank Glorius
- Organisch-Chemisches Institut, University of Münster, Münster, Germany.
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Compound Management and Screening Center, Dortmund, Germany.
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
| |
Collapse
|
9
|
Jiang KL, Liu CM, Nie LT, Jiang HN, Xu L, Zhang KZ, Fan LX, Gao AH, Lin LL, Wang XY, Tan MJ, Zhang QQ, Zhou YB, Li J. Discovery of toxoflavin, a potent IRE1α inhibitor acting through structure-dependent oxidative inhibition. Acta Pharmacol Sin 2023; 44:234-243. [PMID: 35840659 DOI: 10.1038/s41401-022-00949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/24/2022] [Indexed: 01/18/2023] Open
Abstract
Inositol-requiring enzyme 1α (IRE1α) is the most conserved endoplasmic reticulum (ER) stress sensor with two catalytic domains, kinase and RNase, in its cytosolic portion. IRE1α inhibitors have been used to improve existing clinical treatments against various cancers. In this study we identified toxoflavin (TXF) as a new-type potent small molecule IRE1α inhibitor. We used luciferase reporter systems to screen compounds that inhibited the IRE1α-XBP1s signaling pathway. As a result, TXF was found to be the most potent IRE1α RNase inhibitor with an IC50 value of 0.226 μM. Its inhibitory potencies on IRE1α kinase and RNase were confirmed in a series of cellular and in vitro biochemical assays. Kinetic analysis showed that TXF caused time- and reducing reagent-dependent irreversible inhibition on IRE1α, implying that ROS might participate in the inhibition process. ROS scavengers decreased the inhibition of IRE1α by TXF, confirming that ROS mediated the inhibition process. Mass spectrometry analysis revealed that the thiol groups of four conserved cysteine residues (CYS-605, CYS-630, CYS-715 and CYS-951) in IRE1α were oxidized to sulfonic groups by ROS. In molecular docking experiments we affirmed the binding of TXF with IRE1α, and predicted its binding site, suggesting that the structure of TXF itself participates in the inhibition of IRE1α. Interestingly, CYS-951 was just near the docked site. In addition, the RNase IC50 and ROS production in vitro induced by TXF and its derivatives were negative correlated (r = -0.872). In conclusion, this study discovers a new type of IRE1α inhibitor that targets a predicted new alternative site located in the junction between RNase domain and kinase domain, and oxidizes conserved cysteine residues of IRE1α active sites to inhibit IRE1α. TXF could be used as a small molecule tool to study IRE1α's role in ER stress.
Collapse
Affiliation(s)
- Kai-Long Jiang
- Institute of Biomedical Engineering, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Chang-Mei Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Li-Tong Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hai-Ni Jiang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China
| | - Lei Xu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Kun-Zhi Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Zhejiang Center for Medical Device Evaluation, Zhejiang Medical Products Administration, Hangzhou, 311121, China
| | - Li-Xia Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - An-Hui Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lu-Lin Lin
- Institute of Biomedical Engineering, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, China
| | - Xiang-Yu Wang
- The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qi-Qing Zhang
- Institute of Biomedical Engineering, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, China.
| | - Yu-Bo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jia Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China.
- Shanghai Tech University, Shanghai, 201210, China.
| |
Collapse
|
10
|
Wilson IM, Frazier MN, Li JL, Randall TA, Stanley RE. Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants. J Mol Biol 2022; 434:167796. [PMID: 35995266 PMCID: PMC9389836 DOI: 10.1016/j.jmb.2022.167796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022]
Abstract
Global sequencing efforts from the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, continue to provide insight into the evolution of the viral genome. Coronaviruses encode 16 nonstructural proteins, within the first two-thirds of their genome, that facilitate viral replication and transcription as well as evasion of the host immune response. However, many of these viral proteins remain understudied. Nsp15 is a uridine-specific endoribonuclease conserved across all coronaviruses. The nuclease activity of Nsp15 helps the virus evade triggering an innate immune response. Understanding how Nsp15 has changed over the course of the pandemic, and how mutations affect its RNA processing function, will provide insight into the evolution of an oligomerization-dependent endoribonuclease and inform drug design. In combination with previous structural data, bioinformatics analyses of 1.9 + million SARS-CoV-2 sequences revealed mutations across Nsp15's three structured domains (N-terminal, Middle, EndoU). Selected Nsp15 variants were characterized biochemically and compared to wild type Nsp15. We found that mutations to important catalytic residues decreased cleavage activity but increased the hexamer/monomer ratio of the recombinant protein. Many of the highly prevalent variants we analyzed led to decreased nuclease activity as well as an increase in the inactive, monomeric form. Overall, our work establishes how Nsp15 variants seen in patient samples affect nuclease activity and oligomerization, providing insight into the effect of these variants in vivo.
Collapse
Affiliation(s)
- Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA. https://twitter.com/@ishamyana
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA; Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA(†). https://twitter.com/@MNFrazier5
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Thomas A Randall
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
11
|
Wolf EJ, Grünberg S, Dai N, Chen TH, Roy B, Yigit E, Corrêa I. Human RNase 4 improves mRNA sequence characterization by LC–MS/MS. Nucleic Acids Res 2022; 50:e106. [PMID: 35871301 PMCID: PMC9561288 DOI: 10.1093/nar/gkac632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography–mass spectrometry (LC–MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a larger population of uniquely mappable cleavage products. We deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine–two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5′ cap incorporation into in vitro transcribed mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC–MS/MS.
Collapse
Affiliation(s)
- Eric J Wolf
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | | | - Nan Dai
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Tien-Hao Chen
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Bijoyita Roy
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Erbay Yigit
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Ivan R Corrêa
- To whom correspondence should be addressed. Tel: +1 978 380 7504;
| |
Collapse
|
12
|
Ingle S, Chhabra S, Chen J, Lazarus MB, Luo X, Bechhofer DH. Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis. RNA 2022; 28:227-238. [PMID: 34815358 PMCID: PMC8906540 DOI: 10.1261/rna.078962.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The Bacillus subtilis genome is predicted to encode numerous ribonucleases, including four 3' exoribonucleases that have been characterized to some extent. A strain containing gene knockouts of all four known 3' exoribonucleases is viable, suggesting that one or more additional RNases remain to be discovered. A protein extract from the quadruple RNase mutant strain was fractionated and RNase activity was followed, resulting in the identification of an enzyme activity catalyzed by the YloC protein. YloC is an endoribonuclease and is a member of the highly conserved "YicC family" of proteins that is widespread in bacteria. YloC is a metal-dependent enzyme that catalyzes the cleavage of single-stranded RNA, preferentially at U residues, and exists in an oligomeric form, most likely a hexamer. As such, YloC shares some characteristics with the SARS-CoV Nsp15 endoribonuclease. While the in vivo function of YloC in B. subtilis is yet to be determined, YloC was found to act similarly to YicC in an Escherichia coli in vivo assay that assesses decay of the small RNA, RyhB. Thus, YloC may play a role in small RNA regulation.
Collapse
Affiliation(s)
- Shakti Ingle
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Shivani Chhabra
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jiandong Chen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael B Lazarus
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Xing Luo
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David H Bechhofer
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
13
|
de Martin E, Schweizer M. Fifty Shades of Erns: Innate Immune Evasion by the Viral Endonucleases of All Pestivirus Species. Viruses 2022; 14:v14020265. [PMID: 35215858 PMCID: PMC8880635 DOI: 10.3390/v14020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The genus Pestivirus, family Flaviviridae, includes four historically accepted species, i.e., bovine viral diarrhea virus (BVDV)-1 and -2, classical swine fever virus (CSFV), and border disease virus (BDV). A large number of new pestivirus species were identified in recent years. A common feature of most members is the presence of two unique proteins, Npro and Erns, that pestiviruses evolved to regulate the host’s innate immune response. In addition to its function as a structural envelope glycoprotein, Erns is also released in the extracellular space, where it is endocytosed by neighboring cells. As an endoribonuclease, Erns is able to cleave viral ss- and dsRNAs, thus preventing the stimulation of the host’s interferon (IFN) response. Here, we characterize the basic features of soluble Erns of a large variety of classified and unassigned pestiviruses that have not yet been described. Its ability to form homodimers, its RNase activity, and the ability to inhibit dsRNA-induced IFN synthesis were investigated. Overall, we found large differences between the various Erns proteins that cannot be predicted solely based on their primary amino acid sequences, and that might be the consequence of different virus-host co-evolution histories. This provides valuable information to delineate the structure-function relationship of pestiviral endoribonucleases.
Collapse
Affiliation(s)
- Elena de Martin
- Institute of Virology and Immunology, Länggass-Str. 122, POB, CH-3001 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Matthias Schweizer
- Institute of Virology and Immunology, Länggass-Str. 122, POB, CH-3001 Bern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland
- Correspondence:
| |
Collapse
|
14
|
Islam MS, Bandyra KJ, Chao Y, Vogel J, Luisi BF. Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E. RNA 2021; 27:1339-1352. [PMID: 34341070 PMCID: PMC8522691 DOI: 10.1261/rna.078840.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
The conserved endoribonuclease RNase E dominates the dynamic landscape of RNA metabolism and underpins control mediated by small regulatory RNAs in diverse bacterial species. We explored the enzyme's hydrolytic mechanism, allosteric activation, and interplay with partner proteins in the multicomponent RNA degradosome assembly of Escherichia coli. RNase E cleaves single-stranded RNA with preference to attack the phosphate located at the 5' nucleotide preceding uracil, and we corroborate key interactions that select that base. Unexpectedly, RNase E activity is impeded strongly when the recognized uracil is isomerized to 5-ribosyluracil (pseudouridine), from which we infer the detailed geometry of the hydrolytic attack process. Kinetics analyses support models for recognition of secondary structure in substrates by RNase E and for allosteric autoregulation. The catalytic power of the enzyme is boosted when it is assembled into the multienzyme RNA degradosome, most likely as a consequence of substrate capture and presentation. Our results rationalize the origins of substrate preferences of RNase E and illuminate its catalytic mechanism, supporting the roles of allosteric domain closure and cooperation with other components of the RNA degradosome complex.
Collapse
Affiliation(s)
- Md Saiful Islam
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Katarzyna J Bandyra
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Yanjie Chao
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Xuhui district, Shanghai, 200031, China
| | - Jörg Vogel
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| |
Collapse
|
15
|
Tran NH, Carter SD, De Mazière A, Ashkenazi A, Klumperman J, Walter P, Jensen GJ. The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes. Science 2021; 374:52-57. [PMID: 34591618 PMCID: PMC9041316 DOI: 10.1126/science.abh2474] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The signaling network of the unfolded protein response (UPR) adjusts the protein-folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined the in situ structure of IRE1α foci by cryogenic correlated light and electron microscopy combined with electron cryo-tomography and complementary immuno–electron microscopy in mammalian cell lines. IRE1α foci localized to a network of narrow anastomosing ER tubes (diameter, ~28 nm) with complex branching. The lumen of the tubes contained protein filaments, which were likely composed of arrays of IRE1α lumenal domain dimers that were arranged in two intertwined, left-handed helices. This specialized ER subdomain may play a role in modulating IRE1α signaling.
Collapse
Affiliation(s)
- Ngoc-Han Tran
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ann De Mazière
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Corresponding author. (P.W.); (G.J.J.)
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
- Corresponding author. (P.W.); (G.J.J.)
| |
Collapse
|
16
|
Perry JK, Appleby TC, Bilello JP, Feng JY, Schmitz U, Campbell EA. An atomistic model of the coronavirus replication-transcription complex as a hexamer assembled around nsp15. J Biol Chem 2021; 297:101218. [PMID: 34562452 PMCID: PMC8494237 DOI: 10.1016/j.jbc.2021.101218] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 replication-transcription complex is an assembly of nonstructural viral proteins that collectively act to reproduce the viral genome and generate mRNA transcripts. While the structures of the individual proteins involved are known, how they assemble into a functioning superstructure is not. Applying molecular modeling tools, including protein-protein docking, to the available structures of nsp7-nsp16 and the nucleocapsid, we have constructed an atomistic model of how these proteins associate. Our principal finding is that the complex is hexameric, centered on nsp15. The nsp15 hexamer is capped on two faces by trimers of nsp14/nsp16/(nsp10)2, which then recruit six nsp12/nsp7/(nsp8)2 polymerase subunits to the complex. To this, six subunits of nsp13 are arranged around the superstructure, but not evenly distributed. Polymerase subunits that coordinate dimers of nsp13 are capable of binding the nucleocapsid, which positions the 5'-UTR TRS-L RNA over the polymerase active site, a state distinguishing transcription from replication. Analysis of the viral RNA path through the complex indicates the dsRNA that exits the polymerase passes over the nsp14 exonuclease and nsp15 endonuclease sites before being unwound by a convergence of zinc fingers from nsp10 and nsp14. The template strand is then directed away from the complex, while the nascent strand is directed to the sites responsible for mRNA capping. The model presents a cohesive picture of the multiple functions of the coronavirus replication-transcription complex and addresses fundamental questions related to proofreading, template switching, mRNA capping, and the role of the endonuclease.
Collapse
Affiliation(s)
| | | | | | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, California, USA
| | - Uli Schmitz
- Gilead Sciences, Inc, Foster City, California, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| |
Collapse
|
17
|
Chen R, Zhou J, Xie W. Mechanistic Insight into the Peptide Binding Modes to Two M. tb MazF Toxins. Toxins (Basel) 2021; 13:toxins13050319. [PMID: 33925254 PMCID: PMC8145246 DOI: 10.3390/toxins13050319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis (M. tb). It is regarded as a major health threat all over the world, mainly because of its high mortality and drug-resistant nature. Toxin-antitoxin (TA) systems are modules ubiquitously found in prokaryotic organisms, and the well-studied MazEF systems (MazE means “what is it?” in Hebrew) are implicated in the formation of “persister cells” in the M. tb pathogen. Here, we report cocrystal structures of M. tb MazF-mt1 and -mt9, two important MazF members responsible for specific mRNA and tRNA cleavages, respectively, in complexes with truncated forms of their cognate antitoxin peptides. These peptides bind to the toxins with comparable affinities to their full-length antitoxins, which would reduce the RNA-cleavage capacities of the toxins in vitro. After structural analysis of the binding modes, we systemically tested the influence of the substitutions of individual residues in the truncated MazE-mt9 peptide on its affinity. This study provides structural insight into the binding modes and the inhibition mechanisms between the MazE/F-mt TA pairs. More importantly, it contributes to the future design of peptide-based antimicrobial agents against TB and potentially relieves the drug-resistance problems by targeting novel M. tb proteins.
Collapse
Affiliation(s)
- Ran Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510006, China; (R.C.); (J.Z.)
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510006, China; (R.C.); (J.Z.)
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510006, China; (R.C.); (J.Z.)
- Correspondence:
| |
Collapse
|
18
|
Abstract
The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.
Collapse
Affiliation(s)
- Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, UK
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Antonin Tidu
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
| | - Gilbert Eriani
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
| | - Franck Martin
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
| |
Collapse
|
19
|
Pillon MC, Gordon J, Frazier MN, Stanley RE. HEPN RNases - an emerging class of functionally distinct RNA processing and degradation enzymes. Crit Rev Biochem Mol Biol 2021; 56:88-108. [PMID: 33349060 PMCID: PMC7856873 DOI: 10.1080/10409238.2020.1856769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) RNases are an emerging class of functionally diverse RNA processing and degradation enzymes. Members are defined by a small α-helical bundle encompassing a short consensus RNase motif. HEPN dimerization is a universal requirement for RNase activation as the conserved RNase motifs are precisely positioned at the dimer interface to form a composite catalytic center. While the core HEPN fold is conserved, the organization surrounding the HEPN dimer can support large structural deviations that contribute to their specialized functions. HEPN RNases are conserved throughout evolution and include bacterial HEPN RNases such as CRISPR-Cas and toxin-antitoxin associated nucleases, as well as eukaryotic HEPN RNases that adopt large multi-component machines. Here we summarize the canonical elements of the growing HEPN RNase family and identify molecular features that influence RNase function and regulation. We explore similarities and differences between members of the HEPN RNase family and describe the current mechanisms for HEPN RNase activation and inhibition.
Collapse
Affiliation(s)
- Monica C. Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| |
Collapse
|
20
|
Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, Stanley RE. Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun 2021; 12:636. [PMID: 33504779 PMCID: PMC7840905 DOI: 10.1038/s41467-020-20608-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
Collapse
Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas, 77030, USA.
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Seda Kocaman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Cassandra K Hayne
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- Cambridge Institute for Medical Research, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Zachary D Stewart
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Leesa J Deterding
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Venkata P Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| |
Collapse
|
21
|
Peng G, He Y, Wang M, Ashraf MF, Liu Z, Zhuang C, Zhou H. The structural characteristics and the substrate recognition properties of RNase Z S1. Plant Physiol Biochem 2021; 158:83-90. [PMID: 33302124 DOI: 10.1016/j.plaphy.2020.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
TMS5 encodes an RNase ZS1 protein that can process ubiquitin-60S ribosomal protein L40 family (UbL40) mRNAs to regulate thermo-sensitive genic male sterility in rice. Despite the importance of this protein, the structural characteristics and substrate recognition properties of RNase ZS1 remain unclear. Here, we found that the variations in several conservative amino acids alter the activation of RNase ZS1, and its recognition of RNA substrates depends on the structure of RNA. RNase ZS1 acts as a homodimer. The conserved amino acids in or adjacent to enzyme center play a critical role in the enzyme activity of RNase ZS1 and the conserved amino acids that far from active center have little impact on its enzyme activity. The cleavage efficiency of RNase ZS1 for pre-tRNA-MetCAU35 and UbL401 mRNA with cloverleaf-like structure was higher than that of pre-tRNA-AspAUC9 and UbL404 mRNA with imperfect cloverleaf-like structure. This difference implies that the enzyme activity of RNase ZS1 depends on the cloverleaf-like structure of the RNA. Furthermore, the RNase ZS1 activity was not inhibited by the 5' leader sequence and 3' CCA motif of pre-tRNA. These findings provide new insights for studying the cleavage characteristics and substrate recognition properties of RNase ZS.
Collapse
Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Ying He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China.
| |
Collapse
|
22
|
Wang R, Hozumi Y, Yin C, Wei GW. Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. J Chem Inf Model 2020; 60:5853-5865. [PMID: 32530284 PMCID: PMC7318555 DOI: 10.1021/acs.jcim.0c00501] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Indexed: 12/20/2022]
Abstract
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 15 140 genome samples collected up to June 1, 2020, we report that SARS-CoV-2 has undergone 8309 single mutations which can be clustered into six subtypes. We introduce mutation ratio and mutation h-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively nonconservative. In particular, we have identified mutations on 40% of nucleotides in the nucleocapsid gene in the population level, signaling potential impacts on the ongoing development of COVID-19 diagnosis, vaccines, and antibody and small-molecular drugs.
Collapse
Affiliation(s)
- Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Hozumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Changchuan Yin
- Department
of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East
Lansing, Michigan 48824, United States
| |
Collapse
|
23
|
Ulyanova V, Dudkina E, Nadyrova A, Kalashnikov V, Surchenko Y, Ilinskaya O. The Cytotoxicity of RNase-Derived Peptides. Biomolecules 2020; 11:E16. [PMID: 33375305 PMCID: PMC7824363 DOI: 10.3390/biom11010016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial ribonuclease binase exhibits a cytotoxic effect on tumor cells possessing certain oncogenes. The aim of this study was to identify the structural parts of the binase molecule that exert cytotoxicity. Out of five designed peptides, the peptides representing the binase regions 21-50 and 74-94 have the highest cytotoxic potential toward human cervical HeLa and breast BT-20 and MCF-7 cancer cells. The peptides B21-50 and B74-94 were not able to enter human lung adenocarcinoma A549 cells, unlike BT-20 cells, explaining their failure to inhibit A549 cell proliferation. The peptide B74-94 shares similarities with epidermal growth factor (EGF), suggesting the peptide's specificity for EGF receptor overexpressed in BT-20 cells. Thus, the binase-derived peptides have the potential of being further developed as tumor-targeting peptides.
Collapse
Affiliation(s)
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (V.U.); (A.N.); (V.K.); (Y.S.); (O.I.)
| | | | | | | | | |
Collapse
|
24
|
Peng Y, Wang K, Chen J, Wang J, Zhang H, Ze L, Zhu G, Zhao C, Xiao H, Han Z. Identification of a double-stranded RNA-degrading nuclease influencing both ingestion and injection RNA interference efficiency in the red flour beetle Tribolium castaneum. Insect Biochem Mol Biol 2020; 125:103440. [PMID: 32771566 DOI: 10.1016/j.ibmb.2020.103440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 05/10/2023]
Abstract
RNA interference (RNAi) efficiency dramatically varies among different insects and among administration methods. Numerous studies have revealed that a poor RNAi response is usually associated with a high double-stranded RNA (dsRNA)-degrading activity. Using the red flour beetle Tribolium castaneum, we conducted genome-wide identification of genes encoding dsRNA-degrading nucleases of the DNA/RNA non-specific endonuclease superfamily. To achieve a robust RNAi response in T. castaneum, four dsRNase genes were identified in the genome that seemed to be the potential factors reducing RNAi efficacy. Analysis of biochemical properties revealed that optimal conditions for the dsRNA-degrading activity were alkaline (pH 8.0) in the absence of Mg2+ at 37 °C. The dsRNA-degrading activity was predominantly present in the gut, and via heterologous expression and RNAi experimentation, gut-specific TcdsRNase1 was confirmed as the major nuclease performing dsRNA degradation. After a knockdown of the TcdsRNase1 nuclease activity, RNAi efficiency improved from 38.6% to 58.9% and from 20.9% to 53.9% for injection and ingestion of dsRNA, respectively. Our results contribute to a comprehensive understanding of the mechanisms influencing dsRNA stability and even RNAi efficiency in T. castaneum and point to a good method for improving RNAi efficiency through downregulation of the relevant nuclease activity.
Collapse
Affiliation(s)
- Yingchuan Peng
- Institute of Entomology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Kangxu Wang
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiasheng Chen
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinda Wang
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hainan Zhang
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Longji Ze
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanheng Zhu
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington KY, 40546, USA
| | - Chunqing Zhao
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haijun Xiao
- Institute of Entomology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhaojun Han
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
25
|
Ng CS, Kasumba DM, Fujita T, Luo H. Spatio-temporal characterization of the antiviral activity of the XRN1-DCP1/2 aggregation against cytoplasmic RNA viruses to prevent cell death. Cell Death Differ 2020; 27:2363-2382. [PMID: 32034313 PMCID: PMC7370233 DOI: 10.1038/s41418-020-0509-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
Host nucleases are implicated in antiviral response through the processing of pathogen-derived nucleic acids. Among many host RNases, decapping enzymes DCP1 and 2, and 5'→3' exonuclease XRN1, which are components of the RNA decay machinery, have been extensively studied in prokaryotes, plants, and invertebrates but less so in mammalian systems. As a result, the implication of XRN1 and DCPs in viral replication, in particular, the spatio-temporal dynamics during RNA viral infections remains elusive. Here, we highlight that XRN1 and DCPs play a critical role in limiting several groups of RNA viral infections. This antiviral activity was not obvious in wild-type cells but clearly observed in type I interferon (IFN-I)-deficient cells. Mechanistically, infection with RNA viruses induced the enrichment of XRN1 and DCPs in viral replication complexes (vRCs), hence forming distinct cytoplasmic aggregates. These aggregates served as sites for direct interaction between XRN1, DCP1/2, and viral ribonucleoprotein that contains viral RNA (vRNA). Although these XRN1-DCP1/2-vRC-containing foci resemble antiviral stress granules (SGs) or P-body (PB), they did not colocalize with known SG markers and did not correlate with critical PB functions. Furthermore, the presence of 5' mono- and 5' triphosphate structures on vRNA was not required for the formation of XRN1-DCP1/2-vRC-containing foci. On the other hand, single-, double-stranded, and higher-ordered vRNA species play a role but are not deterministic for efficient formation of XRN1-DCP1/2 foci and consequent antiviral activity in a manner proportional to RNA length. These results highlight the mechanism behind the antiviral function of XRN1-DCP1/2 in RNA viral infections independent of IFN-I response, protein kinase R and PB function.
Collapse
Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Dacquin M Kasumba
- Centre de Recherche du Centre Hospitalier de I'Université de Montréal, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Honglin Luo
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
26
|
Kimura H, Kurusu H, Sada M, Kurai D, Murakami K, Kamitani W, Tomita H, Katayama K, Ryo A. Molecular pharmacology of ciclesonide against SARS-CoV-2. J Allergy Clin Immunol 2020; 146:330-331. [PMID: 32593491 PMCID: PMC7293530 DOI: 10.1016/j.jaci.2020.05.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Gunma, Japan.
| | - Hiromu Kurusu
- Advanced Medical Science Research Center, Gunma Paz University, Gunma, Japan
| | - Mitsuru Sada
- Advanced Medical Science Research Center, Gunma Paz University, Gunma, Japan
| | - Daisuke Kurai
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan
| |
Collapse
|
27
|
Park YS, Kim TY, Park H, Lee JH, Nguyen DQ, Hong MK, Lee SH, Kang LW. Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants. Int J Mol Sci 2020; 21:ijms21144926. [PMID: 32664695 PMCID: PMC7404133 DOI: 10.3390/ijms21144926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023] Open
Abstract
The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam antibiotics by producing β-lactamases. Among β-lactamases, metallo-β-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes β-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and β-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.
Collapse
Affiliation(s)
- Yoon Sik Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Tae Yeong Kim
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Myoung-Ki Hong
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
| |
Collapse
|
28
|
Brothers WR, Hebert S, Kleinman CL, Fabian MR. A non-canonical role for the EDC4 decapping factor in regulating MARF1-mediated mRNA decay. eLife 2020; 9:e54995. [PMID: 32510323 PMCID: PMC7279887 DOI: 10.7554/elife.54995] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
EDC4 is a core component of processing (P)-bodies that binds the DCP2 decapping enzyme and stimulates mRNA decay. EDC4 also interacts with mammalian MARF1, a recently identified endoribonuclease that promotes oogenesis and contains a number of RNA binding domains, including two RRMs and multiple LOTUS domains. How EDC4 regulates MARF1 action and the identity of MARF1 target mRNAs is not known. Our transcriptome-wide analysis identifies bona fide MARF1 target mRNAs and indicates that MARF1 predominantly binds their 3' UTRs via its LOTUS domains to promote their decay. We also show that a MARF1 RRM plays an essential role in enhancing its endonuclease activity. Importantly, we establish that EDC4 impairs MARF1 activity by preventing its LOTUS domains from binding target mRNAs. Thus, EDC4 not only serves as an enhancer of mRNA turnover that binds DCP2, but also as a repressor that binds MARF1 to prevent the decay of MARF1 target mRNAs.
Collapse
Affiliation(s)
- William R Brothers
- Lady Davis Institute for Medical Research, Jewish General HospitalMontrealCanada
| | - Steven Hebert
- Lady Davis Institute for Medical Research, Jewish General HospitalMontrealCanada
| | - Claudia L Kleinman
- Lady Davis Institute for Medical Research, Jewish General HospitalMontrealCanada
- Department of Human Genetics, McGill UniversityMontrealCanada
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General HospitalMontrealCanada
- Department of Biochemistry, McGill UniversityMontrealCanada
- Department of Oncology, McGill UniversityMontrealCanada
| |
Collapse
|
29
|
Kang SM, Koo JS, Kim CM, Kim DH, Lee BJ. mRNA Interferase Bacillus cereus BC0266 Shows MazF-Like Characteristics Through Structural and Functional Study. Toxins (Basel) 2020; 12:toxins12060380. [PMID: 32521689 PMCID: PMC7354611 DOI: 10.3390/toxins12060380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 11/16/2022] Open
Abstract
Toxin–antitoxin (TA) systems are prevalent in bacteria and are known to regulate cellular growth in response to stress. As various functions related to TA systems have been revealed, the importance of TA systems are rapidly emerging. Here, we present the crystal structure of putative mRNA interferase BC0266 and report it as a type II toxin MazF. The MazF toxin is a ribonuclease activated upon and during stressful conditions, in which it cleaves mRNA in a sequence-specific, ribosome-independent manner. Its prolonged activity causes toxic consequences to the bacteria which, in turn, may lead to bacterial death. In this study, we conducted structural and functional investigations of Bacillus cereus MazF and present the first toxin structure in the TA system of B. cereus. Specifically, B. cereus MazF adopts a PemK-like fold and also has an RNA substrate-recognizing loop, which is clearly observed in the high-resolution structure. Key residues of B. cereus MazF involved in the catalytic activity are also proposed, and in vitro assay together with mutational studies affirm the ribonucleic activity and the active sites essential for its cellular toxicity.
Collapse
Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Ji Sung Koo
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Chang-Min Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea;
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
- Correspondence: ; Tel.: +82-2-880-7869
| |
Collapse
|
30
|
Foster K, Grüschow S, Bailey S, White MF, Terns MP. Regulation of the RNA and DNA nuclease activities required for Pyrococcus furiosus Type III-B CRISPR-Cas immunity. Nucleic Acids Res 2020; 48:4418-4434. [PMID: 32198888 PMCID: PMC7192623 DOI: 10.1093/nar/gkaa176] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Type III CRISPR-Cas prokaryotic immune systems provide anti-viral and anti-plasmid immunity via a dual mechanism of RNA and DNA destruction. Upon target RNA interaction, Type III crRNP effector complexes become activated to cleave both target RNA (via Cas7) and target DNA (via Cas10). Moreover, trans-acting endoribonucleases, Csx1 or Csm6, can promote the Type III immune response by destroying both invader and host RNAs. Here, we characterize how the RNase and DNase activities associated with Type III-B immunity in Pyrococcus furiosus (Pfu) are regulated by target RNA features and second messenger signaling events. In vivo mutational analyses reveal that either the DNase activity of Cas10 or the RNase activity of Csx1 can effectively direct successful anti-plasmid immunity. Biochemical analyses confirmed that the Cas10 Palm domains convert ATP into cyclic oligoadenylate (cOA) compounds that activate the ribonuclease activity of Pfu Csx1. Furthermore, we show that the HEPN domain of the adenosine-specific endoribonuclease, Pfu Csx1, degrades cOA signaling molecules to provide an auto-inhibitory off-switch of Csx1 activation. Activation of both the DNase and cOA generation activities require target RNA binding and recognition of distinct target RNA 3' protospacer flanking sequences. Our results highlight the complex regulatory mechanisms controlling Type III CRISPR immunity.
Collapse
Affiliation(s)
- Kawanda Foster
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
31
|
Kopp MC, Larburu N, Durairaj V, Adams CJ, Ali MMU. UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor. Nat Struct Mol Biol 2019; 26:1053-1062. [PMID: 31695187 PMCID: PMC6858872 DOI: 10.1038/s41594-019-0324-9] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
BiP is a major endoplasmic reticulum (ER) chaperone and is suggested to act as primary sensor in the activation of the unfolded protein response (UPR). How BiP operates as a molecular chaperone and as an ER stress sensor is unknown. Here, by reconstituting components of human UPR, ER stress and BiP chaperone systems, we discover that the interaction of BiP with the luminal domains of UPR proteins IRE1 and PERK switch BiP from its chaperone cycle into an ER stress sensor cycle by preventing the binding of its co-chaperones, with loss of ATPase stimulation. Furthermore, misfolded protein-dependent dissociation of BiP from IRE1 is primed by ATP but not ADP. Our data elucidate a previously unidentified mechanistic cycle of BiP function that explains its ability to act as an Hsp70 chaperone and ER stress sensor.
Collapse
Affiliation(s)
- Megan C Kopp
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Natacha Larburu
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Vinoth Durairaj
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Christopher J Adams
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Maruf M U Ali
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK.
| |
Collapse
|
32
|
Takeda K, Nagashima S, Shiiba I, Uda A, Tokuyama T, Ito N, Fukuda T, Matsushita N, Ishido S, Iwawaki T, Uehara T, Inatome R, Yanagi S. MITOL prevents ER stress-induced apoptosis by IRE1α ubiquitylation at ER-mitochondria contact sites. EMBO J 2019; 38:e100999. [PMID: 31368599 PMCID: PMC6669929 DOI: 10.15252/embj.2018100999] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/01/2019] [Accepted: 05/15/2019] [Indexed: 11/09/2022] Open
Abstract
Unresolved endoplasmic reticulum (ER) stress shifts the unfolded protein response signaling from cell survival to cell death, although the switching mechanism remains unclear. Here, we report that mitochondrial ubiquitin ligase (MITOL/MARCH5) inhibits ER stress-induced apoptosis through ubiquitylation of IRE1α at the mitochondria-associated ER membrane (MAM). MITOL promotes K63-linked chain ubiquitination of IRE1α at lysine 481 (K481), thereby preventing hyper-oligomerization of IRE1α and regulated IRE1α-dependent decay (RIDD). Therefore, under ER stress, MITOL depletion or the IRE1α mutant (K481R) allows for IRE1α hyper-oligomerization and enhances RIDD activity, resulting in apoptosis. Similarly, in the spinal cord of MITOL-deficient mice, ER stress enhances RIDD activity and subsequent apoptosis. Notably, unresolved ER stress attenuates IRE1α ubiquitylation, suggesting that this directs the apoptotic switch of IRE1α signaling. Our findings suggest that mitochondria regulate cell fate under ER stress through IRE1α ubiquitylation by MITOL at the MAM.
Collapse
Affiliation(s)
- Keisuke Takeda
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Shun Nagashima
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Isshin Shiiba
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Aoi Uda
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Takeshi Tokuyama
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Naoki Ito
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Toshifumi Fukuda
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Nobuko Matsushita
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Satoshi Ishido
- Department of MicrobiologyHyogo College of MedicineNishinomiyaJapan
| | - Takao Iwawaki
- Medical Research InstituteKanazawa Medical UniversityIshikawaJapan
| | - Takashi Uehara
- Department of Medicinal PharmacologyGraduate School of Medicine, Dentistry, and Pharmaceutical SciencesOkayama UniversityOkayamaJapan
| | - Ryoko Inatome
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| | - Shigeru Yanagi
- Laboratory of Molecular BiochemistrySchool of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
| |
Collapse
|
33
|
Wang Q, Groenendyk J, Paskevicius T, Qin W, Kor KC, Liu Y, Hiess F, Knollmann BC, Chen SRW, Tang J, Chen XZ, Agellon LB, Michalak M. Two pools of IRE1α in cardiac and skeletal muscle cells. FASEB J 2019; 33:8892-8904. [PMID: 31051095 PMCID: PMC6662970 DOI: 10.1096/fj.201802626r] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/08/2019] [Indexed: 12/23/2022]
Abstract
The endoplasmic reticulum (ER) plays a central role in cellular stress responses via mobilization of ER stress coping responses, such as the unfolded protein response (UPR). The inositol-requiring 1α (IRE1α) is an ER stress sensor and component of the UPR. Muscle cells also have a well-developed and highly subspecialized membrane network of smooth ER called the sarcoplasmic reticulum (SR) surrounding myofibrils and specialized for Ca2+ storage, release, and uptake to control muscle excitation-contraction coupling. Here, we describe 2 distinct pools of IRE1α in cardiac and skeletal muscle cells, one localized at the perinuclear ER and the other at the junctional SR. We discovered that, at the junctional SR, calsequestrin binds to the ER luminal domain of IRE1α, inhibiting its dimerization. This novel interaction of IRE1α with calsequestrin, one of the highly abundant Ca2+ handling proteins at the junctional SR, provides new insights into the regulation of stress coping responses in muscle cells.-Wang, Q., Groenendyk, J., Paskevicius, T., Qin, W., Kor, K. C., Liu, Y., Hiess, F., Knollmann, B. C., Chen, S. R. W., Tang, J., Chen, X.-Z., Agellon, L. B., Michalak, M. Two pools of IRE1α in cardiac and skeletal muscle cells.
Collapse
Affiliation(s)
- Qian Wang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jody Groenendyk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Wenying Qin
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Kaylen C. Kor
- Division of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yingjie Liu
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Florian Hiess
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bjorn C. Knollmann
- Division of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - S. R. Wayne Chen
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jingfeng Tang
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Xing-Zhen Chen
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada; and
| | - Luis B. Agellon
- School of Human Nutrition, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| |
Collapse
|
34
|
Zhang Z, Chen LQ, Zhao YL, Yang CG, Roundtree IA, Zhang Z, Ren J, Xie W, He C, Luo GZ. Single-base mapping of m 6A by an antibody-independent method. Sci Adv 2019; 5:eaax0250. [PMID: 31281898 PMCID: PMC6609220 DOI: 10.1126/sciadv.aax0250] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/30/2019] [Indexed: 05/12/2023]
Abstract
N 6-methyladenosine (m6A) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput m6A identification method depends on the anti-m6A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of m6A. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease-Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic, single-base m6A maps generated by m6A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual m6A sites, confirming the high reliability and accuracy of m6A-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that m6A sites are conserved with single-nucleotide specificity and tend to cluster among species.
Collapse
Affiliation(s)
- Zhang Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li-Qian Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu-Li Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai-Guang Yang
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ian A. Roundtree
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Zijie Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Jian Ren
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chuan He
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Corresponding author.
| |
Collapse
|
35
|
Colombano G, Caldwell JJ, Matthews TP, Bhatia C, Joshi A, McHardy T, Mok NY, Newbatt Y, Pickard L, Strover J, Hedayat S, Walton MI, Myers SM, Jones AM, Saville H, McAndrew C, Burke R, Eccles SA, Davies FE, Bayliss R, Collins I. Binding to an Unusual Inactive Kinase Conformation by Highly Selective Inhibitors of Inositol-Requiring Enzyme 1α Kinase-Endoribonuclease. J Med Chem 2019; 62:2447-2465. [PMID: 30779566 PMCID: PMC6437697 DOI: 10.1021/acs.jmedchem.8b01721] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Indexed: 12/19/2022]
Abstract
A series of imidazo[1,2- b]pyridazin-8-amine kinase inhibitors were discovered to allosterically inhibit the endoribonuclease function of the dual kinase-endoribonuclease inositol-requiring enzyme 1α (IRE1α), a key component of the unfolded protein response in mammalian cells and a potential drug target in multiple human diseases. Inhibitor optimization gave compounds with high kinome selectivity that prevented endoplasmic reticulum stress-induced IRE1α oligomerization and phosphorylation, and inhibited endoribonuclease activity in human cells. X-ray crystallography showed the inhibitors to bind to a previously unreported and unusually disordered conformation of the IRE1α kinase domain that would be incompatible with back-to-back dimerization of the IRE1α protein and activation of the endoribonuclease function. These findings increase the repertoire of known IRE1α protein conformations and can guide the discovery of highly selective ligands for the IRE1α kinase site that allosterically inhibit the endoribonuclease.
Collapse
Affiliation(s)
- Giampiero Colombano
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - John J. Caldwell
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Thomas P. Matthews
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Chitra Bhatia
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Amar Joshi
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Tatiana McHardy
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Ngai Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Yvette Newbatt
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Lisa Pickard
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Jade Strover
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Somaieh Hedayat
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Michael I. Walton
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Stephanie M. Myers
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Alan M. Jones
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Harry Saville
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Suzanne A. Eccles
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Faith E. Davies
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Richard Bayliss
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
- School
of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit and Division of Molecular Pathology, The Institute of Cancer Research, London SW7 3RP, U.K.
| |
Collapse
|
36
|
Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A. The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res 2018; 46:1958-1972. [PMID: 29346615 PMCID: PMC5829648 DOI: 10.1093/nar/gky003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/25/2017] [Accepted: 01/03/2018] [Indexed: 11/14/2022] Open
Abstract
Four different types (α4, α'2, (αβ)2 and ϵ2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αβ)2 and ϵ2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αβ)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and β subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (αβ)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (αβ)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.
Collapse
Affiliation(s)
- Ayano Kaneta
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Wataru Morikazu
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
37
|
Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M. Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components. Nat Commun 2018; 9:97. [PMID: 29311576 PMCID: PMC5758563 DOI: 10.1038/s41467-017-02570-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/11/2017] [Indexed: 01/08/2023] Open
Abstract
Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.
Collapse
Affiliation(s)
- Michal Razew
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Michal Taube
- Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Mariusz Czarnocki-Cieciura
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Elzbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Kawinska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Jakub Piatkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Pawel Golik
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Maciej Kozak
- Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
| |
Collapse
|
38
|
Song S, Hong S, Jang J, Yeom JH, Park N, Lee J, Lim Y, Jeon JY, Choi HK, Lee M, Ha NC, Lee K. Functional implications of hexameric assembly of RraA proteins from Vibrio vulnificus. PLoS One 2017; 12:e0190064. [PMID: 29261778 PMCID: PMC5738090 DOI: 10.1371/journal.pone.0190064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
RNase E has a pivotal role in the degradation and processing of RNAs in Escherichia coli, and protein inhibitors RraA and RraB control its enzymatic activity. The halophilic pathogenic bacterium Vibrio vulnificus also expresses orthologs of RNase E and RraA—RNase EV, RraAV1, and RraAV2 (herein renamed as VvRNase E, VvRraA1, and VvRraA2). A previous study showed that VvRraA1 actively inhibits the ribonucleolytic activity of VvRNase E by interacting with the C-terminal region of VvRNase E. However, the molecular mechanism underlying the effect of VvRraA1 on the ribonucleolytic activity of VvRNase E has not yet been elucidated. In this study, we report that the oligomer formation of VvRraA proteins affects binding efficiency to VvRNase E as well as inhibitory activity on VvRNase E action. The hexameric structure of VvRraA1 was converted to lower oligomeric forms when the Cys 9 residue was substituted with an Asp residue (VvRraA1-C9D), showing decreased inhibitory activity of VvRraA1 on VvRNase E in vivo. These results indicated that the intermolecular disulfide linkage contributed critically to the hexamerization of VvRraA1 for its proper function. On the contrary, the VvRraA2 that existed in a trimeric state did not bind to or inhibit VvRNase E. An in vitro cleavage assay further showed the reduced inhibitory effect of VvRraA-C9D on VvRNase E activity compared to wild-type VvRraA1. These findings provide insight into how VvRraA proteins can regulate VvRNase E action on its substrate RNA in V. vulnificus. In addition, based on structural and functional comparison of RraA homologs, we suggest that hexameric assembly of RraA homologs may well be required for their action on RNase E-like proteins.
Collapse
Affiliation(s)
- Saemee Song
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Seokho Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jinyang Jang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Nohra Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Yeri Lim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Jun-Yeong Jeon
- School of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Hyung-Kyoon Choi
- School of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- * E-mail: (NCH); (KL)
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
- * E-mail: (NCH); (KL)
| |
Collapse
|
39
|
Saramago M, Peregrina A, Robledo M, Matos RG, Hilker R, Serrania J, Becker A, Arraiano CM, Jiménez-Zurdo JI. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. Nucleic Acids Res 2017; 45:1371-1391. [PMID: 28180335 PMCID: PMC5388416 DOI: 10.1093/nar/gkw1234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 01/23/2023] Open
Abstract
Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.
Collapse
Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
- These authors contributed equally to the work as the first authors
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Rolf Hilker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Cecilia M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - José I. Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- To whom correspondence should be addressed. Tel: +34 958181600; Fax: +34 958181609;
| |
Collapse
|
40
|
Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CW. The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily. Nucleic Acids Res 2017; 45:5013-5025. [PMID: 28398546 PMCID: PMC5435912 DOI: 10.1093/nar/gkx230] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 01/01/2023] Open
Abstract
Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIYkris complex from Yersinia kristensenii ATCC 33638. CdiA-CTYkris adopts the same fold as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Consistent with the structural homology, CdiA-CTYkris has potent RNase activity in vitro and in vivo. Structure-guided mutagenesis reveals that His175, Arg186, Thr276 and Tyr278 contribute to CdiA-CTYkris activity, suggesting that these residues participate in substrate binding and/or catalysis. CdiIYkris binds directly over the putative active site and likely neutralizes toxicity by blocking access to RNA substrates. Significantly, CdiA-CTYkris is the first non-vertebrate protein found to possess the RNase A superfamily fold, and homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria. These observations suggest that RNase A-like toxins are commonly deployed in inter-bacterial competition.
Collapse
Affiliation(s)
- Gaëlle Batot
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- These authors contributed equally to this work as first authors
| | - Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- These authors contributed equally to this work as first authors
| | - Greg Ekberg
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
- These authors contributed equally to this work as first authors
| | - Ervin M. Irimpan
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Grazyna Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Celia W. Goulding
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
- To whom correspondence should be addressed. Tel: +1 949 824 0337; Fax: +1 949 824 8551
| |
Collapse
|
41
|
Abstract
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.
Collapse
Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
42
|
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 2017; 23:655-672. [PMID: 28138060 PMCID: PMC5393176 DOI: 10.1261/rna.060368.116] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 01/26/2017] [Indexed: 05/21/2023]
Abstract
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.
Collapse
Affiliation(s)
- Zhichao Miao
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France;
| | - Ryszard W Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Maciej Antczak
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA
| | - Alexander J Becka
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marcin Biesiada
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Michał J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Clarence Yu Cheng
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stanisław Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Caleb Geniesse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kalli Kappel
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Grzegorz E Łach
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - François Major
- Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Thomas H Mann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marcin Magnus
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | | | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Katarzyna J Purzycka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Aiming Ren
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Greggory M Rice
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
| | - John Santalucia
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- DNA Software, Ann Arbor, Michigan 48104, USA
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Arpit Tandon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeremiah J Trausch
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA
| | - Siqi Tian
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jian Wang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
| | - Benfeard Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yi Xiao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaojun Xu
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Tomasz Zok
- Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France;
| |
Collapse
|
43
|
Seo S, Kim D, Song W, Heo J, Joo M, Lim Y, Yeom JH, Lee K. RraAS1 inhibits the ribonucleolytic activity of RNase ES by interacting with its catalytic domain in Streptomyces coelicolor. J Microbiol 2016; 55:37-43. [PMID: 28035598 DOI: 10.1007/s12275-017-6518-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 11/26/2022]
Abstract
RraA is a protein inhibitor of RNase E, which degrades and processes numerous RNAs in Escherichia coli. Streptomyces coelicolor also contains homologs of RNase E and RraA, RNase ES and RraAS1/RraAS2, respectively. Here, we report that, unlike other RraA homologs, RraAS1 directly interacts with the catalytic domain of RNase ES to exert its inhibitory effect. We further show that rraAS1 gene deletion in S. coelicolor results in a higher growth rate and increased production of actinorhodin and undecylprodigiosin, compared with the wild-type strain, suggesting that RraAS1-mediated regulation of RNase ES activity contributes to modulating the cellular physiology of S. coelicolor.
Collapse
Affiliation(s)
- Sojin Seo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Daeyoung Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jihune Heo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yeri Lim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| |
Collapse
|
44
|
Hilal T, Yamamoto H, Loerke J, Bürger J, Mielke T, Spahn CM. Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. Nat Commun 2016; 7:13521. [PMID: 27995908 PMCID: PMC5187420 DOI: 10.1038/ncomms13521] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 01/13/2023] Open
Abstract
The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways.
Collapse
Affiliation(s)
- Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Max-Planck Institut für Molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Thorsten Mielke
- Max-Planck Institut für Molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Christian M.T. Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
45
|
Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DBT, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 2016; 353:aaf5573. [PMID: 27256883 PMCID: PMC5127784 DOI: 10.1126/science.aaf5573] [Citation(s) in RCA: 1285] [Impact Index Per Article: 160.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guided ribonuclease function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, mutations of which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.
Collapse
Affiliation(s)
- Omar O Abudayyeh
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvana Konermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian M Slaymaker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B T Cox
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ekaterina Semenova
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia. Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Feng Zhang
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA. Departments of Brain and Cognitive Science and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
46
|
Ilinskaya ON, Singh I, Dudkina E, Ulyanova V, Kayumov A, Barreto G. Direct inhibition of oncogenic KRAS by Bacillus pumilus ribonuclease (binase). Biochim Biophys Acta 2016; 1863:1559-67. [PMID: 27066977 DOI: 10.1016/j.bbamcr.2016.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 11/18/2022]
Abstract
RAS proteins function as molecular switches that transmit signals from cell surface receptors into specific cellular responses via activation of defined signaling pathways (Fang, 2015). Aberrant constitutive RAS activation occurs with high incidence in different types of cancer (Bos, 1989). Thus, inhibition of RAS-mediated signaling is extremely important for therapeutic approaches against cancer. Here we showed that the ribonuclease (RNase) binase, directly interacts with endogenous KRAS. Further, molecular structure models suggested an inhibitory nature of binase-RAS interaction involving regions of RAS that are important for different aspects of its function. Consistent with these models, phosphorylation analysis of effectors of RAS-mediated signaling revealed that binase inhibits the MAPK/ERK signaling pathway. Interestingly, RAS activation assays using a non-hydrolysable GTP analog (GTPγS) demonstrated that binase interferes with the exchange of GDP by GTP. Furthermore, we showed that binase reduced the interaction of RAS with the guanine nucleotide exchange factor (GEF), SOS1. Our data support a model in which binase-KRAS interaction interferes with the function of GEFs and stabilizes the inactive GDP-bound conformation of RAS thereby inhibiting MAPK/ERK signaling. This model plausibly explains the previously reported, antitumor-effect of binase specific towards RAS-transformed cells and suggests the development of anticancer therapies based on this ribonuclease.
Collapse
Affiliation(s)
- Olga N Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal (Volga-Region) University, Kremlevskaya str. 18, 420008, Kazan, Russia
| | - Indrabahadur Singh
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Elena Dudkina
- Institute of Fundamental Medicine and Biology, Kazan Federal (Volga-Region) University, Kremlevskaya str. 18, 420008, Kazan, Russia.
| | - Vera Ulyanova
- Institute of Fundamental Medicine and Biology, Kazan Federal (Volga-Region) University, Kremlevskaya str. 18, 420008, Kazan, Russia
| | - Airat Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal (Volga-Region) University, Kremlevskaya str. 18, 420008, Kazan, Russia
| | - Guillermo Barreto
- Institute of Fundamental Medicine and Biology, Kazan Federal (Volga-Region) University, Kremlevskaya str. 18, 420008, Kazan, Russia; LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Germany; German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Germany.
| |
Collapse
|
47
|
Piperi C, Adamopoulos C, Papavassiliou AG. XBP1: A Pivotal Transcriptional Regulator of Glucose and Lipid Metabolism. Trends Endocrinol Metab 2016; 27:119-122. [PMID: 26803729 DOI: 10.1016/j.tem.2016.01.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/12/2022]
Abstract
X-box binding protein 1 (XBP1) is a major, well-conserved component of the unfolded protein response (UPR) that is crucial for glucose homeostasis and lipid metabolism. Metabolic dysfunction has been associated with XBP1 transcriptional activity. Recently, compounds selectively targeting the IRE1α-XBP1 pathway have emerged as a potential approach for treatment of metabolic diseases.
Collapse
Affiliation(s)
- Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Adamopoulos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| |
Collapse
|
48
|
Niewoehner O, Jinek M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA 2016; 22:318-29. [PMID: 26763118 PMCID: PMC4748810 DOI: 10.1261/rna.054098.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/14/2023]
Abstract
Prokaryotic CRISPR-Cas systems provide an RNA-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. In type III-A CRISPR-Cas systems, the RNA-guided multisubunit Csm effector complex targets both single-stranded RNAs and double-stranded DNAs. In addition to the Csm complex, efficient anti-plasmid immunity mediated by type III-A systems also requires the CRISPR-associated protein Csm6. Here we report the crystal structure of Csm6 from Thermus thermophilus and show that the protein is a ssRNA-specific endoribonuclease. The structure reveals a dimeric architecture generated by interactions involving the N-terminal CARF and C-terminal HEPN domains. HEPN domain dimerization leads to the formation of a composite ribonuclease active site. Consistently, mutations of invariant active site residues impair catalytic activity in vitro. We further show that the ribonuclease activity of Csm6 is conserved across orthologs, suggesting that it plays an important functional role in CRISPR-Cas systems. The dimer interface of the CARF domains features a conserved electropositive pocket that may function as a ligand-binding site for allosteric control of ribonuclease activity. Altogether, our work suggests that Csm6 proteins provide an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems that operates in conjunction with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex.
Collapse
Affiliation(s)
- Ole Niewoehner
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| |
Collapse
|
49
|
Sheppard NF, Glover CVC, Terns RM, Terns MP. The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. RNA 2016; 22:216-24. [PMID: 26647461 PMCID: PMC4712672 DOI: 10.1261/rna.039842.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 05/15/2023]
Abstract
Prokaryotes are frequently exposed to potentially harmful invasive nucleic acids from phages, plasmids, and transposons. One method of defense is the CRISPR-Cas adaptive immune system. Diverse CRISPR-Cas systems form distinct ribonucleoprotein effector complexes that target and cleave invasive nucleic acids to provide immunity. The Type III-B Cmr effector complex has been found to target the RNA and DNA of the invader in the various bacterial and archaeal organisms where it has been characterized. Interestingly, the gene encoding the Csx1 protein is frequently located in close proximity to the Cmr1-6 genes in many genomes, implicating a role for Csx1 in Cmr function. However, evidence suggests that Csx1 is not a stably associated component of the Cmr effector complex, but is necessary for DNA silencing by the Cmr system in Sulfolobus islandicus. To investigate the function of the Csx1 protein, we characterized the activity of recombinant Pyrococcus furiosus Csx1 against various nucleic acid substrates. We show that Csx1 is a metal-independent, endoribonuclease that acts selectively on single-stranded RNA and cleaves specifically after adenosines. The RNA cleavage activity of Csx1 is dependent upon a conserved HEPN motif located within the C-terminal domain of the protein. This motif is also key for activity in other known ribonucleases. Collectively, the findings indicate that invader silencing by Type III-B CRISPR-Cas systems relies both on RNA and DNA nuclease activities from the Cmr effector complex as well as on the affiliated, trans-acting Csx1 endoribonuclease.
Collapse
Affiliation(s)
- Nolan F Sheppard
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Claiborne V C Glover
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA Department of Genetics, University of Georgia, Athens, Georgia 30602, USA Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
50
|
Xie X, Dubrovsky EB. Knockout of Drosophila RNase ZL impairs mitochondrial transcript processing, respiration and cell cycle progression. Nucleic Acids Res 2015; 43:10364-75. [PMID: 26553808 PMCID: PMC4666369 DOI: 10.1093/nar/gkv1149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/20/2015] [Indexed: 11/15/2022] Open
Abstract
RNase Z(L) is a highly conserved tRNA 3'-end processing endoribonuclease. Similar to its mammalian counterpart, Drosophila RNase Z(L) (dRNaseZ) has a mitochondria targeting signal (MTS) flanked by two methionines at the N-terminus. Alternative translation initiation yields two protein forms: the long one is mitochondrial, and the short one may localize in the nucleus or cytosol. Here, we have generated a mitochondria specific knockout of the dRNaseZ gene. In this in vivo model, cells deprived of dRNaseZ activity display impaired mitochondrial polycistronic transcript processing, increased reactive oxygen species (ROS) and a switch to aerobic glycolysis compensating for cellular ATP. Damaged mitochondria impose a cell cycle delay at the G2 phase disrupting cell proliferation without affecting cell viability. Antioxidants attenuate genotoxic stress and rescue cell proliferation, implying a critical role for ROS. We suggest that under a low-stress condition, ROS activate tumor suppressor p53, which modulates cell cycle progression and promotes cell survival. Transcriptional profiling of p53 targets confirms upregulation of antioxidant and cycB-Cdk1 inhibitor genes without induction of apoptotic genes. This study implicates Drosophila RNase Z(L) in a novel retrograde signaling pathway initiated by the damage in mitochondria and manifested in a cell cycle delay before the mitotic entry.
Collapse
Affiliation(s)
- Xie Xie
- Department of Biology, Fordham University, Bronx, NY 10458, USA
| | - Edward B Dubrovsky
- Department of Biology, Fordham University, Bronx, NY 10458, USA Center for Cancer, Genetic Diseases, and Gene Regulation, Fordham University, Bronx, NY 10458, USA
| |
Collapse
|